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We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species--but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora.

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We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species.

Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species.

We identified 21, 716 unique insertions across the three species. Of all insertions considered, the majority (approximately 80%) are unique to one species (Figure 2). There is a strong consistency in the distribution of copies among TE families. LTR elements are the most common type, making up roughly 59% of all TEs; DNA elements comprise 19%; Helitron and non-LTR elements approximately 11% each (Figure 3a). The closely related A. thaliana and A. lyrata also show no difference in the relative abundance of families [31]. In both genera, non-LTRs are the smallest contributors to the TE load in the genomes. However, in Arabidopsis the DNA elements dominate (including Helitrons) making up over 55% of all TEs, consistent with the reported expansion of the Basho Helitrons in A. thaliana[45].

Here, we report results from a whole genome study of TE abundance and distributions in multiple individuals in three species from the plant genus Capsella. Comparing population samples from the outcrosser C. grandiflora to two of its self-compatible relatives allows us to begin to empirically dissect the population and genome wide effects of a mating system shift in driving TE evolution.

The evolution of selfing does not appear to have had the same effect in the two self-compatible Capsella species. Perhaps the most striking result of this study is the consistently lower TE copy numbers in the self-compatible C. orientalis. This reduction is apparent for all families and in both centromeric regions and along chromosome arms (Figure 3), as well as for recent insertions near genes (Figure 4). Furthermore, C. orientalis shows a detectable absence of rare and an excess of common TE insertions (Figure 5). The present transposition rate thus appears to be very low in C. orientalis. TE accumulation is known to be a key driver of genome size evolution in plants [3, 48] and this reduction in transposition rate may in part explain why C. orientalis has the smallest genome in the genus [38].

In contrast to C. orientalis, C. rubella does not appear to be TE poorer than C. grandiflora. Instead, there is a trend of an increase in copy number, which seems to be due to higher accumulation in centromeric regions (Figure 3), although this observation may also be due to poorer mapping of the other species in these regions. However, when we consider only insertions near genes, which are where recent insertions tend to reside, C. grandiflora has a higher abundance than C. rubella (Figure 4). Capsella rubella also has the highest excess of rare insertions, although this trend is most pronounced along the chromosome arms (Figure 5). This may reflect an increase in transposition rate or be a product of the recent population bottleneck C. rubella experienced in conjunction with the evolution of selfing [40, 49].

Taken together our results suggest that the effects of mating system on transposon evolution may vary from case to case. A candidate factor determining the direction of the effect may the age of the selfing lineage. Finally, cross-species comparisons of transposon abundance are sensitive to reference genome bias and caution must be applied when using re-sequencing approaches.

Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences.

We determined that TEs comprise ~25% of the genome. The predominant class of TEs (~12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome.

Recently, the genome of Heliconius melpomene was released [8], providing new insights into lepidopteran genome evolution from a transposable element perspective. H. melpomene is a heliconiine butterfly that is widespread throughout Central America and South America [8, 9]. The H. melpomene genome is the third lepidopteran and second butterfly genome to be sequenced. Unfortunately, the analysis of the second genome (and the first butterfly), the monarch, Danaus plexipus, was not comprehensive [10]. Therefore, we confine our comparisons of the H. melpomene genome to B. mori.

Our analyses indicate that H. melpomene exhibits a high rate of TE turnover, with little accumulation of older elements, especially longer, autonomous elements, suggesting that TEs have an overall deleterious effect on the genome. Furthermore, the TE landscape of H. melpomene is distinct compared to the silkworm moth, consisting of substantially higher Class II content and a distinct set of retrotransposons. This suggests that lepidopterans in general will exhibit high levels of TE diversity as additional genomes are sequenced and characterized.

TEs comprise ~25% of the H. melpomene genome (Table 1). The majority are non-LTR retrotransposons (12.07% of the genome), and among these, Short INterspersed Elements (SINEs) make up the greatest proportion (8.22%). The second most common group in H. melpomene are the DNA transposons, comprising 10.05% of the genome and dominated by Helitrons (~5.37% of the genome). LTR elements were also found, but occupy a much smaller proportion of the genome (0.45%).

Autonomous non-LTR elements exhibit a similar lack of recent activity with mean periods of activity ranging from ~2.7 mya to over 21 mya (Additional file 2: Table S1). A general lack of retrotransposition competence is suggested when examining numbers of potentially intact ORFs. We were unable to identify intact ORFs for most autonomous retrotransposon families and, of the families with identifiable, intact ORFs, the numbers were generally small. The largest number of intact ORFs was for RTE-3_Hm, with six (Table 3). The lack of success in identifying intact ORFs could be attributed to problems with the assembly. Most breaks in an assembly are associated with highly similar TE insertions. However, we were able to identify multiple instances of relatively long and highly similar sequences (see the discussion of Tc3-1_Hm below), suggesting instead that intact non-LTR ORFs, if present, would not evade detection. 17dc91bb1f